Search result: Catalogue data in Spring Semester 2018
Biology Master  | ||||||
 Elective Major Subject Areas | ||||||
| Elective Major: Structural Biology and Biophysics | ||||||
| Compulsory Concept Courses | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 551-0307-01L | Molecular and Structural Biology II: From Gene to Protein D-BIOL students are obliged to take part I and part II as a two-semester course. | O | 3 credits | 2V | N. Ban, F. Allain, M. Pilhofer | |
| Abstract | This course will cover advanced topics in molecular biology and biochemistry with emphasis on the structure and function of cellular assemblies involved in expression and maintenance of genetic information. We will cover the architecture and the function of molecules involved in DNA replication, transcription, translation, nucleic acid packaging in viruses, RNA processing, and CRISPER/CAS system. | |||||
| Learning objective | Students will gain a deep understanding of large cellular assemblies and the structure-function relationships governing their function in fundamental cellular processes ranging from DNA replication, transcription and translation. The lectures throughout the course will be complemented by exercises and discussions of original research examples to provide students with a deeper understanding of the subjects and to encourage active student participation. | |||||
| Content | Advanced class covering the state of the research in structural molecular biology of basic cellular processes with emphasis on the function of large cellular assemblies. | |||||
| Lecture notes | Updated handouts will be provided during the class. | |||||
| Literature | The lecture will be based on the latest literature. Additional suggested literature: Branden, C., and J. Tooze, Introduction to Protein Structure, 2nd ed. (1995). Garland, New York. | |||||
| Elective Compulsory Concept Courses See D-BIOL Master Studies Guide | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 529-0732-00L | Proteins and Lipids | W | 6 credits | 3G | D. Hilvert | |
| Abstract | An overview of the relationship between protein sequence, conformation and function. | |||||
| Learning objective | Overview of the relationship between protein sequence, conformation and function. | |||||
| Content | Proteins, structures and properties, (bio)synthesis of polypeptides, protein folding and design, protein engineering, chemical modification of proteins, proteomics. | |||||
| Literature | General Literature: - T.E. Creighton: Proteins: Structures and Molecular Properties, 2nd Edition, H.W. Freeman and Company, New York, 1993. - C. Branden, J. Tooze , Introduction to Protein Structure, Garland Publishing, New York, 1991. - J. M. Berg, J. L. Tymoczko, L. Stryer: Biochemistry, 5th edition, H.W. Freeman and Company, New York, 2002. - G.A. Petsko, D. Ringe: Protein Structure and Function, New Science Press Ltd., London, 2004. Original Literature: Citations from the original literature relevant to the individual lectures will be assigned weekly. | |||||
| 551-0320-00L | Cellular Biochemistry (Part II) | W | 3 credits | 2V | Y. Barral, R. Kroschewski, A. E. Smith | |
| Abstract | This course will focus on molecular mechanisms and concepts underlying cellular biochemistry, providing advanced insights into the structural and functional details of individual cell components, and the complex regulation of their interactions. Particular emphasis will be on the spatial and temporal integration of different molecules and signaling pathways into global cellular processes. | |||||
| Learning objective | The full-year course (551-0319-00 & 551-0320-00) focuses on the molecular mechanisms and concepts underlying the biochemistry of cellular physiology, investigating how these processes are integrated to carry out highly coordinated cellular functions. The molecular characterization of complex cellular functions requires a combination of approaches such as biochemistry, but also cell biology and genetics. This course is therefore the occasion to discuss these techniques and their integration in modern cellular biochemistry. The students will be able to describe the structural and functional details of individual cell components, and the spatial and temporal regulation of their interactions. In particular, they will learn to explain how different molecules and signaling pathways can be integrated during complex and highly dynamic cellular processes such as intracellular transport, cytoskeletal rearrangements, cell motility, and cell division. In addition, they will be able to illustrate the relevance of particular signaling pathways for cellular pathologies such as cancer or during cellular infection. | |||||
| Content | Spatial and temporal integration of different molecules and signaling pathways into global cellular processes, such as cell division, cell infection and cell motility. Emphasis is also put on the understanding of pathologies associated with defective cell physiology, such as cancer or during cellular infection. | |||||
| Literature | Recommended supplementary literature (review articles and selected primary literature) will be provided during the course. | |||||
| Prerequisites / Notice | To attend this course the students must have a solid basic knowledge in chemistry, biochemistry, cell biology and general biology. Biology students have in general already attended the first part of the "Cellular Biochemistry" concept course (551-0319-00). The course will be taught in English. In addition, the course will be based on a blended-learning scenario, where frontal lectures will be complemented with carefully chosen web-based teaching elements that students access through the ETH Moodle platform. | |||||
| 551-0314-00L | Microbiology (Part II) | W | 3 credits | 2V | W.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, J. Vorholt-Zambelli | |
| Abstract | Advanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Learning objective | This concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Content | Advanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis. | |||||
| Lecture notes | Updated handouts will be provided during the class. | |||||
| Literature | Current literature references will be provided during the lectures. | |||||
| Prerequisites / Notice | English | |||||
| 551-0324-00L | Systems Biology | W | 6 credits | 4V | R. Aebersold, B. Christen, M. Claassen, U. Sauer | |
| Abstract | Introduction to experimental and computational methods of systems biology. By using baker’s yeast as a thread through the series, we focus on global methods for analysis of and interference with biological functions. Illustrative applications to other organisms will highlight medical and biotechnological aspects. | |||||
| Learning objective | - obtain an overview of global analytical methods - obtain an overview of computational methods in systems biology - understand the concepts of systems biology | |||||
| Content | Overview of global analytical methods (e.g. DNA arrays, proteomics, metabolomics, fluxes etc), global interference methods (siRNA, mutant libraries, synthetic lethality etc.) and imaging methods. Introduction to mass spectrometry and proteomics. Concepts of metabolism in microbes and higher cells. Systems biology of developmental processes. Concepts of mathematical modeling and applications of computational systems biology. | |||||
| Lecture notes | no script | |||||
| Literature | The course is not taught by a particular book, but some books are suggested for further reading: - Systems biology in Practice by Klipp, Herwig, Kowald, Wierling und Lehrach. Wiley-VCH 2005 | |||||
| Elective Compulsory Master Courses | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 551-1402-00L | Molecular and Structural Biology VI: Biophysical Analysis of Macromolecular Mechanisms This course is strongly recommended for the Masters Major "Biology and Biophysics". | W | 4 credits | 2V | R. Glockshuber, T. Ishikawa, S. Jonas, B. Schuler, E. Weber-Ban | |
| Abstract | The course is focussed on biophysical methods for characterising conformational transitions and reaction mechanisms of proteins and biological mecromolecules, with focus on methods that have not been covered in the Biology Bachelor Curriculum. | |||||
| Learning objective | The goal of the course is to give the students a broad overview on biopyhsical techniques available for studying conformational transitions and complex reaction mechanisms of biological macromolecules. The course is particularly suited for students enrolled in the Majors "Structural Biology and Biophysics", "Biochemistry" and "Chemical Biology" of the Biology MSc curriculum, as well as for MSc students of Chemistry and Interdisciplinary Natural Sciences". | |||||
| Content | The biophysical methods covered in the course include advanced reaction kinetics, methods for the thermodynamic and kinetic analysis of protein-ligand interactions, classical and dynamic light scattering, analytical ultracentrifugation, spectroscopic techniques such as fluorescence anisotropy, fluorescence resonance energy transfer (FRET) and single molecule fluorescence spectrosopy, modern electron microscopy techniques, atomic force microscopy, and isothermal and differential scanning calorimetry. | |||||
| Lecture notes | Course material from the individual lecturers wil be made available at the sharepoint website https://team.biol.ethz.ch/e-learn/551-1402-00L | |||||
| Prerequisites / Notice | Finished BSc curriculum in Biology, Chemistry or Interdisciplinary Natural Sciences. The course is also adequate for doctoral students with research projects in structural biology, biophysics, biochemistry and chemical biology. | |||||
| 551-0224-00L | Advanced Proteomics  For master students from the 2nd semester on, also doctoral candidates and post docs. | W | 4 credits | 6G | R. Aebersold, L. Gillet, M. Gstaiger, A. Leitner, P. Pedrioli | |
| Abstract | Goal of the course is to analyze current and newly emerging technologies and approaches in protein and proteome analysis with regard to their application in biology, biotechnology and medicine. Format: Introduction by instructor followed by discussions stimulated by reading assignments and exercises. | |||||
| Learning objective | To discuss current and newly emerging technologies and approaches in protein and proteome analysis with regard to their applications in biology, biotechnology, medicine and systems biology. | |||||
| Content | Block course teaching current methods for the acquisition and processing of proteomic datasets. | |||||
| Prerequisites / Notice | Number of people: Not exceeding 30. Students from ETHZ, Uni Zurich and University of Basel Non-ETH students must register at ETH Zurich as special students http://www.rektorat.ethz.ch/students/admission/auditors/index_EN | |||||
| 551-0364-00L | Functional Genomics Information for UZH students: Enrolment to this course unit only possible at ETH. No enrolment to module BIO 254 at UZH. Please mind the ETH enrolment deadlines for UZH students: Link | W | 3 credits | 2V | C. von Mering, C. Beyer, B. Bodenmiller, M. Gstaiger, H. Rehrauer, R. Schlapbach, K. Shimizu, N. Zamboni, further lecturers | |
| Abstract | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. | |||||
| Learning objective | Functional genomics is key to understanding the dynamic aspects of genome function and regulation. Functional genomics approaches use the wealth of data produced by large-scale DNA sequencing, gene expression profiling, proteomics and metabolomics. Today functional genomics is becoming increasingly important for the generation and interpretation of quantitative biological data. Such data provide the basis for systems biology efforts to elucidate the structure, dynamics and regulation of cellular networks. | |||||
| Content | The curriculum of the Functional Genomics course emphasizes an in depth understanding of new technology platforms for modern genomics and advanced genetics, including the application of functional genomics approaches such as advanced microarrays, proteomics, metabolomics, clustering and classification. Students will learn quality controls and standards (benchmarking) that apply to the generation of quantitative data and will be able to analyze and interpret these data. The training obtained in the Functional Genomics course will be immediately applicable to experimental research and design of systems biology projects. | |||||
| Prerequisites / Notice | The Functional Genomics course will be taught in English. | |||||
| 551-1100-00L | Infectious Agents: From Molecular Biology to Disease Number of participants limited to 22. Requires application; selected applicants will be notified before the first week of lectures. | W | 4 credits | 2S | W.‑D. Hardt, L. Eberl, U. F. Greber, A. B. Hehl, M. Kopf, S. R. Leibundgut, C. Münz, A. Oxenius, P. Sander | |
| Abstract | Literature seminar for students at the masters level and PhD students. Introduction to the current research topics in infectious diseases; Introduction to key pathogens which are studied as model organisms in this field; Overview over key research groups in the field of infectious diseases in Zürich. | |||||
| Learning objective | Working with the current research literature. Getting to know the key pathogens serving as model organisms and the research technologies currently used in infection biology. | |||||
| Content | for each model pathogen (or key technology): 1. introduction to the pathogen 2. Discussion of one current research paper. The paper will be provided by the respective supervisor. He/she will give advice (if required) and guide the respective literature discussion. | |||||
| Lecture notes | Teachers will provide the research papers to be discussed. Students will prepare handouts for the rest of the group for their assigned seminar. | |||||
| Literature | Teachers will provide the research papers to be discussed. | |||||
| Prerequisites / Notice | Restricted to max 22 students. Please sign up until two weeks before the beginning of the semester via e-mail to micro_secr@micro.biol.ethz.ch and include the following information: 551-1100-00L; your name, your e-mail address, university/eth, students (specialization, semester), PhD students (research group, member of a PhD program? which program?). The 22 students admitted to this seminar will be selected and informed by e-mail in the week befor the beginning of the semester by W.-D. Hardt. The first seminar date will serve to form groups of students and assign a paper to each group. | |||||
| 551-1404-00L | RNA and Proteins: Post-Transcriptional Regulation of Gene Expression (University of Zurich) No enrolment to this course at ETH Zurich. Book the corresponding module directly at UZH. UZH Module Code: BCH252 Mind the enrolment deadlines at UZH: https://www.uzh.ch/cmsssl/en/studies/application/mobilitaet.html | W | 3 credits | 2V | University lecturers | |
| Abstract | The course introduces the cellular processes and molecular mechanisms involved in regulating genome expression at the post-transcriptional level. Topics will include : -RNA processing, and transport; -protein synthesis and translational control, trafficking and degradation; -RNA-guided regulation (RNA interference, microRNAs); -molecular surveillance and quality control mechanisms | |||||
| Learning objective | -Outline the cellular processes used by eukaryotic and prokaryotic cells to control gene expression at the post- transcriptional level. -Describe the molecular mechanisms underlying post-transcriptional gene regulation -Identify experimental approaches used to study post-transcriptional gene regulation and describe their strengths and weaknesses. | |||||
| 551-1412-00L | Molecular and Structural Biology IV: Visualizing Macromolecules by X-ray Crystallography and EM | W | 4 credits | 2V | N. Ban, D. Böhringer, T. Ishikawa, M. A. Leibundgut, K. Locher, M. Pilhofer, K. Wüthrich | |
| Abstract | This course provides an in-depth discussion of two main methods to determine the 3D structures of macromolecules and complexes at high resolution: X-ray crystallography and cryo-electron microscopy. Both techniques result in electron density maps that are interpreted by atomic models. | |||||
| Learning objective | Students will obtain the theoretical background to understand structure determination techniques employed in X-ray crystallography and electron microscopy, including diffraction theory, crystal growth and analysis, reciprocal space calculations, interpretation of electron density, structure building and refinement as well as validation. The course will also provide an introduction into the use of cryo-electron tomography to visualize complex cellular substructures at sub-nanometer resolutions, effectively bridging the resolution gap between optical microscopy and single particle cryo-electron microscopy. Lectures will be complemented with practical sessions where students will have a chance to gain hands on experience with sample preparation, data processing and structure building and refinement. | |||||
| 551-1414-00L | Molecular and Structural Biology V: Studying Macromolecules by NMR and EPR | W | 4 credits | 2V | F. Allain, A. D. Gossert, G. Jeschke, K. Wüthrich | |
| Abstract | The course provides an overview of experimental methods for the determination of structures of macromolecules at atomic resolution in solution. The two main methods used are Nuclear Magnetic Resonance (NMR) spectroscopy and Electron Paramagnetic Resonance (EPR) spectroscopy. | |||||
| Learning objective | Insight into the methodology, areas of application and limitations of these two methods for the structure determination of biological macromolecules. Practical exercises with spectra to have hands on understanding of the methodology. | |||||
| Content | Part I: Methods for the determination of protein structures in solution using nuclear magnetic resonance (NMR) spectroscopy. Experimental approaches to the characterization of intramolecular dynamics of proteins. Part II: NMR methods for structurally characterizing RNA and protein-RNA complexes. Part III: EPR of biomolecules | |||||
| Literature | 1) Wüthrich, K. NMR of Proteins and Nucleic Acids, Wiley-Interscience. 2) Dominguez et al, Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61. 3) Duss O et al, Methods Enzymol. 2015;558:279-331. | |||||
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